ArticlePlant & cell physiology2021
Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing.
Article in Plant & cell physiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
- Genomic insights into the medieval cultivation history of influential high-yielding Asian rice.Scientific reports · 2026Article
- Amylose content in rice: integrating genetics, grain filling physiology, and breeding strategies.Frontiers in plant science · 2026Review
- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- QTN detection and candidate gene identification for improved eating and cooking quality in rice using GWAS and PLS regression analysis.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.PLoS genetics · 2024Article
- Development of SNP genotyping assays for heading date in rice.Breeding science · 2024Article
- Development of genomic and genetic resources facilitating molecular genetic studies on untapped Myanmar rice germplasms.Breeding science · 2024Article
- Metabolic diversity analysis and genome wide assessment of oxalate accumulation in the leaves of rice (Plant biotechnology (Tokyo, Japan) · 2024Article
- Functions and mechanisms of RNA tailing by nucleotidyl transferase proteins in plants.Frontiers in plant science · 2024Review
- CRISPR-Cas9-based repeat depletion for high-throughput genotyping of complex plant genomes.Genome research · 2023Article
- Identifying genetically redundant accessions in the world's largest cassava collection.Frontiers in plant science · 2023Article
- Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species.Rice (New York, N.Y.) · 2022Article
- Transposable element finder (TEF): finding active transposable elements from next generation sequencing data.BMC bioinformatics · 2022Article
- Identification of a unique allele in the quantitative trait locus for crown root number inBreeding science · 2022Article
- GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea.Frontiers in genetics · 2022Article
- Artificial selection in the expansion of rice cultivation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
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12 authors.
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Abstract
The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole-genome resequencing of these 50 accessions and obtained a total of 2,145,095 single nucleotide polymorphism (SNPs) and 317,832 insertion-deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+, to examine the haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed genome-wide association studies (GWAS) for agronomical traits using the JRC and another core collection, the World Rice Core Collection (WRC), comprising 69 accessions also provided by the NARO genebank. In leaf blade width, a strong peak close to NAL1, a key gene for the regulation of leaf width, and, in heading date, a peak near HESO1 involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC + WRC. Thus, JRC and JRC + WRC are suitable populations for GWAS of particular traits.
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